R: Options Settings

options {spam} | R Documentation

## Options Settings

### Description

Allow the user to set and examine a variety of options which affect the way in which R computes and displays sparse matrix results.

### Details

Invoking `options()` with no arguments returns a list with the current values of the options. To access the value of a single option, one should use `getOption("spam.eps")`, e.g., rather than `options("spam.eps")` which is a list of length one.

Of course, printing is still subordinate to `getOption("max.print")` or similar options.

### Value

For `getOption`, the current value set for option `x`, or `NULL` if the option is unset.

For `options()`, a list of all set options sorted by category. For `options(name)`, a list of length one containing the set value, or `NULL` if it is unset. For uses setting one or more options, a list with the previous values of the options changed (returned invisibly).

### Options used for the package `spam`

A short description with the default values follows.

`spam.eps=.Machine$double.eps`:

  values smaller than this are considered as zero. This is only used when creating spam objects.

`spam.drop=FALSE`:

  default parameter for `drop` when subsetting

`spam.printsize=100`:

  the max number of elements of a matrix which we display as regular matrix.

`spam.imagesize=10000`:

  the max number of elements of a matrix we display as regular matrix with `image` or `display`. Larger matrices are represented as dots only.

`spam.cex=1200`:

  default dot size for `image` or `display`.

`spam.structurebased=FALSE`:

  should operations be carried out on the nonzero entries (the structure) or including the zeros.

`spam.inefficiencywarning=1e6`:

  issue a warning when inefficient operations are performed and the matrix exceeds the specified size. Valid value is a postive integer or a logical. `TRUE` corresponds to 1 (always), `FALSE` to `Inf`.

`spam.trivalues=FALSE`:

  a flag whether to return the structure (`FALSE`) or the values themselves (`TRUE`) when returning the upper and lower triangular part of a matrix.

`spam.listmethod="PE"`:

  algorithm for `spam.list`. Default is suggestion by Paul Eilers (thanks). Any other specification uses a bubble sort algorithm which is only slightly faster for very sparse matrices.

`spam.dopivoting=TRUE`:

  default parameter for "`solve`" routines. `FALSE` would solve the system without using the permutation.

`spam.NAOK=FALSE`:

  logical determines if `NA`, `NaN` and `Inf` are allowed to Fortan. Setting to `TRUE` allows to work with these but full functionality has not been tested.

`spam.safemodevalidity=TRUE`:

  logical determines if sanity check is peformed when constructing sparse matrices. Default is safer but somewhat slower.

`spam.cholsymmetrycheck=TRUE`:

  for the Cholesky factorization, verify if the matrix is symmetric.

`spam.cholpivotcheck=TRUE`:

  for the Cholesky factorization, when passing a permutation, should a minimum set of checks be performed?

`spam.cholupdatesingular="warning"`:

  for a Cholesky update, what happens if the matrix is singular: `"warning"` only and returning the not updated factor, `"error"` or return simply `"NULL"`.

`spam.cholincreasefactor=c(1.25,1.25)`:

  If not enought memory could be allocated, these are the steps to increase it.

`spam.nnznearestdistnnz=c(400^2,400)`:

  Memory allocation parameters for `nearest.dist`.

`spam.nearestdistincreasefactor=1.25`:

  If not enought memory could be allocated, this is the step to increase it.

### See Also

Functions influenced by these options include: `print.spam`, `display.spam`, `image.spam`, `upper.tri.spam`, `chol.spam`, `nearest.dist`, etc.
`powerboost`

### Examples

    smat <- diag.spam( 1:8)
    smat
    options(spam.printsize=49)
    smat

    # List all spam options:
    options()[grep("spam",names(options()))]

    # Reset to default values:
    options(spam.eps=.Machine$double.eps,
            spam.drop=FALSE,
            spam.printsize=100,
            spam.imagesize=10000,
            spam.cex=1200,
            spam.structurebased=FALSE,
            spam.inefficiencywarning=1e6,
            spam.trivalues=FALSE,
            spam.listmethod="PE",
            spam.NAOK=FALSE,
            spam.safemodevalidity=TRUE,
            spam.dopivoting=TRUE,
            spam.cholsymmetrycheck=TRUE,
            spam.cholpivotcheck=TRUE,
            spam.cholupdatesingular="warning",
            spam.cholincreasefactor=c(1.25,1.25),
            spam.nearestdistincreasefactor=1.25,
            spam.nearestdistnnz=c(400^2,400))

[Package spam version 2.3-0 Index]